4NPD

High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.

Deis, L.N.Pemble, C.W.Qi, Y.Hagarman, A.Richardson, D.C.Richardson, J.S.Oas, T.G.

(2014) Structure 22: 1467-1477

  • DOI: 10.1016/j.str.2014.08.014
  • Primary Citation of Related Structures:  
    4NPF, 4NPD, 4NPE

  • PubMed Abstract: 
  • The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bu ...

    The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bundle domains (E-D-A-B-C) separated by conserved flexible linkers. Prior attempts to crystallize individual domains in the absence of a binding partner have apparently been unsuccessful. There have also been no previous structures of tandem domains. Here we report the high-resolution crystal structures of a single C domain, and of two B domains connected by the conserved linker. Both structures exhibit extensive multiscale conformational heterogeneity, which required novel modeling protocols. Comparison of domain structures shows that helix1 orientation is especially heterogeneous, coordinated with changes in side chain conformational networks and contacting protein interfaces. This represents the kind of structural plasticity that could enable SpA to bind multiple partners.


    Organizational Affiliation

    Department of Biochemistry, Duke University, Durham, NC 27710, USA. Electronic address: oas@duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein AA58Staphylococcus aureusMutation(s): 0 
Gene Names: protein Aspa
Find proteins for P38507 (Staphylococcus aureus)
Explore P38507 
Go to UniProtKB:  P38507
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.25α = 90
b = 38.41β = 117.44
c = 28.61γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description